Reverted to global alignment for haplotype-haplotype alignments
Merge branch 'master' of /nfs/users/nfs_c/caa/source/sga-basequals
Using quality scores is now a command line option
Fixed DindelHaplotype::extractVariants() incorrect assertion
Merge branch 'quality-scores'
Merge branch 'master' of /nfs/users/nfs_j/js18/work/git_repository/sga
fixing alignment bug
Perform semi-global haplotype realignment within dindel
Fixed inf bug in genotyping
Updated examples to use ropebwt
Update README to credit Heng's ropebwt implementation
Updated sga-index help text
Merge branch 'master' of github.com:jts/sga
Ropebwt algorithm now uses the command line threading parameter
Merge branch 'ropebwt'
ropebwt: .sai file is now written, reversed index can be constructed
Merge branch 'master' into quality-scores
BWT writing now function in ropebwt
Genotyping in multisample caller seems to work.
Wrote a new VCFCollections wrapper to pass sample names to Dindel
Integrating Heng Li's ropebwt code
Merge pull request #22 from nathanhaigh/master
Minor STDOUT updates
Merge remote-tracking branch 'upstream/master'
Additional info (algorithm used) sent to STDOUT when using SAIS - thi…
…s is to be consistent with the output when BCR is used.
Send info about which file is being processed to STDOUT.
Set GraphCompare verbosity to the user's requested value
Integrated quality scores into the variant calling pipeline
Started implementation of quality scores for variant calling pipeline
Fixed GCC 4.6 warnings
Merge pull request #20 from nathanhaigh/master
merge pull request 20